some basic questions about ICE normalization

[biozzq]

Dear @NelleV

Some questions about the HiC normalization have confused me a long time. As the normalization is critical for the correct identification of different chromation interactions between samples, so I here want to ask you for help. Thank you very much.

1 Does ICE normalization take sequence depth into account?
2 Is there any differences between normalization by chromosome and by genome-wide? Which pipeline can generate more comparable results among different chromosomes?

sincerely,
Zheng zhuqing

[ZHIDIHUAYUAN]

Hi,
I met with the same problem. I want to analysis the differences between two allele in MHC region. The data I have was the sequences of two haplotypes, so I can get the SNP information in MHC. First, I run the HiC-pro with the SNP info of MHC in allele-specific mode. So I got two contact maps about MHC region. But how can I normalize them ? Do you have any suggestions?
Thanks